Genetic Diversity in Passiflora Species Assessed by Morphological and ITS Sequence Analysis
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Hindawi Publishing Corporation e Scientific World Journal Volume 2014, Article ID 598313, 11 pages http://dx.doi.org/10.1155/2014/598313 Research Article Genetic Diversity in Passiflora Species Assessed by Morphological and ITS Sequence Analysis Shiamala Devi Ramaiya,1 Japar Sidik Bujang,1 and Muta Harah Zakaria2 1 Department of Animal Science and Fisheries, Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia Bintulu Sarawak Campus, 97008 Bintulu, Sarawak, Malaysia 2 Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Shiamala Devi Ramaiya; shiamala [email protected] Received 16 January 2014; Revised 13 May 2014; Accepted 15 May 2014; Published 22 June 2014 Academic Editor: Andrea Zuccolo Copyright © 2014 Shiamala Devi Ramaiya et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edu li s with high levels of genetic similarity; in contrast, P. fo eti d a was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. fo eti d a from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of rphologicalmo assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level. 1. Introduction undergone significant revision based on morphological traits by Feuillet and MacDougal [7] and four subgenera were rec- Passiflora is extensively grown in tropical and subtropical ognized: Passiflora, Decaloba, Deidamioides, and Astrophea. regions of the world. More than 500 species in this genus have While progress has been made in understanding phylogenetic been identified, and most of them are distributed throughout relationships of subgenus Passiflora, little is known about Central and South America [1]. Colombia is one of the main the relationship among them. The subgenus Passiflora is the centers of Passiflora diversity which accommodates more largest in genus of Passiflora which comprised about 240 than 100 species and is rich in nearly all sections of the species generally regarded as typical passionflowers. Species genus [2]. Passiflora species have been cultivated for their of subgenus Passiflora are characterized by handsome flowers edible fruits, ornamental flowers, and pharmaceutical uses. that are dominated by corona [1]. Feuillet and MacDougal The Passiflora genus contains the highest number of species [7] subdivide the representatives of subgenus Passiflora into in Passifloraceae with edible fruit [3]; in addition, the plants six supersections and further divided into sections or series of this genus have desirable organoleptic properties [4]. based on their morphological characteristics. At the early 20th century, two major technical mono- The species of the Passiflora genus have a wide range graphs laid the modern foundation for Passiflora systematics, of morphological characteristics, anatomical differences, and including works by Harms [5]andKillip[6]. The species were phylogenetic variability. According to Sanchez´ et al. [8], divided into 22 subgenera based on floral morphology by Passiflora species are difficult to classify because some species Killip [6]. Later, the infrageneric taxonomy of Passiflora has vary widely in terms of morphology and other species closely 2 The Scientific World Journal resemble each other. Taxonomic classifications of Passiflora subgenus Passiflora and DNA studies using sequence data aretypicallybasedonmorphological[9–11], ecological [12], from the genome may more accurately define this phylogeny. and agronomic variations [13]. For example, P. e du li s is Accessing molecular polymorphisms at the species level also generally characterized according to production, fruit weight, contributes to the acquisition of knowledge that can be fruit size, juiciness, and juice acidity; however, these variables useful for the conservation of the diversity of Passiflora. do not represent precise quantitative traits at the taxonomic Interest in this agronomically important crop (particularly level [9]. Moreover, existing inter- and intraspecies dissimi- in the Passiflora subgenus) has grown. Therefore, we studied larity among the Passiflora species makes understanding the morphological characteristics and phylogenetic relationships link between morphological plasticity, genotypic diversity, of species of this genus by evaluating the genetic diversity andspeciationchallenging.Increasingnumbersofvarious and comparing the ITS sequence data from plants of different interspecific hybrids have been produced in this genus [14], origins. The knowledge generated by these genetic-based thus contributing to broad morphological variability. characterizations provides information on the parental selec- Germplasm characterization based on molecular phy- tion for breeding works and also may contribute to various logeny can also contribute to a better understanding of the aspects of future biological and ecological studies. evolutionary process and genetic divergence of accessions. Assessing genetic diversity in Passiflora is also important for the utilization and conservation of the germplasm. The 2. Materials and Methods genetic background of the plant is a crucial factor for plant 2.1. Sample Collection and Morphological Analysis. Plant breeders when selecting the parental material for breeding materials were obtained from various regions of East [15, 16]. Over the years, studies have been carried out to Malaysia as presented in Table 1.Plantpartsfromcultivated examine the phylogenetic relationships within the genera. Passiflora accessions P. e du li s producing purple fruits (PE1), Studies have reported attempts to clearly demarcate the P. e du li s producing dark purple fruits (PE2), P. incar nata , P. species of the Passiflora genus using restriction enzymes quadrangularis and P. malifor mi s were collected from the fruit (cpDNA sites; Yockteng and Nadot [17]; Paikrao et al. [18]), farm of Universiti Putra Malaysia Bintulu Sarawak Campus amplified fragments length polymorphism markers (AFLP; ∘ ∘ (UPMKB) Bintulu (N 03 12.45 and E 113 4.68 ), Sarawak. Ortiz et al. [4]; Segura et al. [15]), microsatellite markers The five plant species were grown from seeds acquired from (SSR; Ortiz et al. [4]; Oliveira et al. [19]), and inter-simple the commercial supplier Trade Winds Fruit, Windsor. In sequence repeats (ISSR; dos Santos et al. [11]).However,the addition, P. e du li s producing pink red fruits (PE3) and P. genetic diversity of Passiflora species is mostly estimated with edulis producing yellow fruits (PE4) were collected from random amplified polymorphic DNA (RAPD; Fajardo et al. ∘ small-scale passion fruit farms at Kota Kinabalu (N 05 58.28 [20]; Aukar et al. [21]; Crochemore et al. [22]; Cerqueira-Silva ∘ ∘ and E 116 5.72 ), Sabah and Ba’kelalan (N 03 58.44 and et al. [23]). ∘ E 115 37.08 ), Sarawak, respectively. Wild P. fo eti d a possessing The internal transcribed spacer (ITS) region of the flowers with green bracts (PF1) and P. fo eti d a possessing nuclear ribosomal 18S-5.8S-25S rDNA locus, which has been flowers with red bracts (PF2) were collected from bushes used in phylogenetic studies of many angiosperm families, ∘ ∘ at Bintulu (N 03 10.25 and E 113 2.39 ), Sarawak. Data has proven particularly useful for improving our under- on vegetative and reproductive morphology were recorded, standing of interspecies relationships [24]. The two internal and quantitative features were determined for the aril parts; transcribed spacer DNA sequences have evolved rapidly and leaves, stems, tendrils, bracts, flowers, fruits and seeds. are therefore useful for comparing closely related taxa. In Specimen identification and botanical nomenclature were some genera, variations in ITS sequences have proven useful based on the taxonomic keys of Ulmer and MacDougal [1]. for studies at the species level [25]. The ITS region is also flanked by well-conserved rRNA genes that can be used to differentiate plant species [26]suchaslentils[27], peanuts 2.2. Phylogenetic Analysis [28], maize [29], and seagrass [30]. The ITS regions have also been used to assess the phylogeny of the genus Passiflora. 2.2.1. Polymerase Chain Reaction (PCR) Amplification. DNA In particular, a recent study by Mader¨ et al. [31]used was isolated from 0.01 g of fresh leaves